fMRI Slice Timing

Owned by Paul Macey (admin)
Last updated: Dec 29, 2021 by Paul Macey
1 min read

CSPM can do slice timing correction if the slice times are available in DICOM (as of 2020-03 only recent Siemens files) or a settings file is in the raw data folder. The file should be labelled “slicetiming*.txt”.

Priority is:

  1. Manual settings (see below); this is 1st priority since Siemens 7T info is invalid as of 2020-03.

  2. BIDS “SliceTiming” (from mriconvert)

  3. DICOM header info (only works for some DICOM files)

Slice timing (prefix “a”)

Slice timing does temporal smoothing to adjust for differences in the times of slice acquisition. The slice times are available in recent Siemens files (Prisma, not Trio), some BIDS files as converted by dcm2nii (comes with mricron), or manually in a settings file.

Settings file: slicetiming.txt

  • Contains the slice times

  • Store with raw data (converted to nifti)

  • Manually created (CSPM => fMRI => “Slice Timing - Create Settings”)

    • Snapshot on right

  • Save in raw data “nifti” folder

    • Prior to 2020-09, this was saved in the “raw” (or “DICOM”, “PARREC”) folder

  • Copied to project “rawimages” with fMRI nifti files during Project “Copy and Coreg”

  • Copied to project “fMRIpreprocess” with fMRI nifti files during Preprocessing

  • Applied during Slice timing correction step

    • Will fail with error if no slice timing information is available

Create a settings file

You’ll need number of slices, slice order, and TR.